Table 2 CDR3–FR4 sequences identified by de novo peptide sequencing.

No.	Qualified peptides	TBLASTN_hit	FR4_matched	CDR3_matched	Putative de novo
1	AHGSSTDHWGQGTLVTVSSAS	Yes	Yes	No	Yes
2	AHGSSESHWGQGTLVTVSSAS	Yes	Yes	No	Yes
3	HWGQGTLVTVSSAST	Yes	Yes	No	(Yes)
4	VWGQGTTVTVSSAS	Yes	Yes	N/A
5	DVPWGQGTLVTVSS	Yes	Yes	No	Yes
6	LWGLGTLVTVSSA	Yes	No	N/A	Yes
7	YWGQGTLVTVSS	Yes	Yes	N/A
8	WGQGTLVTVSS	Yes	Yes	N/A
9	YWGQGTPVTVS	Yes	N/A	N/A
10	WGQGTLVTVS	Yes	N/A	N/A

N/A: not applicable.
(Yes): “unclassified due to insufficient CDR3 length”.
The local confidence of each amino acid constituting the peptide was ≥80%. VH sequences in the CDR3 region and CDR3 anchor amino acids are indicated in black underlined and bold characters, respectively. “TBLASTN_hit” indicates whether the J gene germline reference sequence search via a TBLASTN homology search found a match. “FR4_matched” indicates whether the flag for the FR4 region in each peptide matched the FR4 region in the cDNA database. “CDR3_matched” indicates whether the flag for the CDR3 region in each peptide matched the CDR3 region in the cDNA database. “Putative de novo” indicates whether the peptide is a putative de novo peptide.
Abbreviations used in this article:.
aPAP, autoimmune PAP.
CDR, complementarity determining region.
FR, framework region.
GM-CSF, granulocyte-macrophage colony-stimulating factor.
GMAb, GM-CSF autoantibody.
GMARBs, GM-CSF autoreactive B cells.
IgG, immunoglobulin G.
IgG-HV, variable region of immunoglobulin G heavy chain.
IMGT, the international ImMunoGeneTics information system.
LC/MS/MS, liquid chromatography coupled with tandem mass spectrometry.
PAP, pulmonary alveolar proteinosis.
PBMCs, peripheral blood mononuclear cells.
PCR, polymerase chain reaction.
TBS, tris-buffered saline.
TIMS-TOF, trapped ion mobility spectrometry coupled with quadrupole time-of-flight mass spectrometry.

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